TY - JOUR T1 - Single-molecule sequencing and conformational capture enable <em>de novo</em> mammalian reference genomes JF - bioRxiv DO - 10.1101/064352 SP - 064352 AU - Derek M. Bickhart AU - Benjamin D. Rosen AU - Sergey Koren AU - Brian L. Sayre AU - Alex R. Hastie AU - Saki Chan AU - Joyce Lee AU - Ernest T. Lam AU - Ivan Liachko AU - Shawn T. Sullivan AU - Joshua N. Burton AU - Heather J. Huson AU - Christy M. Kelley AU - Jana L. Hutchison AU - Yang Zhou AU - Jiajie Sun AU - Alessandra Crisà AU - F. Abel Ponce De León AU - John C. Schwartz AU - John A. Hammond AU - Geoffrey C. Waldbieser AU - Steven G. Schroeder AU - George E. Liu AU - Maitreya J. Dunham AU - Jay Shendure AU - Tad S. Sonstegard AU - Adam M. Phillippy AU - Curtis P. Van Tassell AU - Timothy P.L. Smith Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/07/18/064352.abstract N2 - The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a &gt;250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species. ER -